Gavin Massey put Colchester ahead after just two minutes, but Jed Wallace's volley levelled the scores three minutes later.
Sam Sodje's clumsy tackle on Freddie Sears handed Colchester a penalty, which Sears coolly dispatched after 15 minutes before Massey's deflected strike made it 3-1 to Colchester five minutes later.
James Keene pulled one back for Pompey after 73 minutes, but their second-half pressure wasn't enough to prevent a seventh straight defeat.
Whittingham, left fuming with his side's commitment in the first half, said: "If we're not careful, we're in danger of just being pleased we put in a good performance in the second half.
"Well, that's not good enough. You've got to give a good performance in the first and second half to win games."
Whittingham added: "There was just no commitment in the first half. All you ask of players when they do something is that they commit to it.
"We weren't committed to running forward, we weren't committed to challenges, we weren't committed to playing the ball forward and we weren't committed to making decent crosses.
"You can talk about commitment in different ways, but when someone goes into a challenge, you can see whether they're committed or not.
"When the ball is bouncing around and no-one is committing themselves that last little bit just to go and win it, put a head on it or put a foot on it, you can't excuse that."